rs1464853

Variant names:

• chr7-70954832-A-G
• rs1464853

Your query was ambiguous. Multiple possible variants found:

• chr7-70954832-A-G
• chr7-70954832-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.556 in 152,026 control chromosomes in the GnomAD database, including 24,504 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84555 AN: 151908 Hom.: 24502 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.586

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.556 AC: 84582 AN: 152026 Hom.: 24504 Cov.: 32 AF XY: 0.560 AC XY: 41658 AN XY: 74324

African (AFR) AF: 0.383 AC: 15895 AN: 41454

American (AMR) AF: 0.545 AC: 8321 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2242 AN: 3468

East Asian (EAS) AF: 0.654 AC: 3378 AN: 5166

South Asian (SAS) AF: 0.592 AC: 2844 AN: 4804

European-Finnish (FIN) AF: 0.759 AC: 8026 AN: 10572

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.618 AC: 41987 AN: 67988

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.592 Hom.: 76901

Bravo AF: 0.539

Asia WGS AF: 0.576 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.79
PhyloP100		-0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1464853; hg19: chr7-70419818;